The field of the disclosure relates to microbiology. In particular, the field relates to detection of drug resistance in microorganisms. The field also relates to biochemical analysis by mass spectrometry.
Bioinformatics derives knowledge from computer analysis of biological data. This can consist of the information stored in the genetic code, but also experimental results from various sources, patient statistics, and scientific literature. Research in bioinformatics includes method development for storage, retrieval, and analysis of the data. Bioinformatics is a rapidly developing branch of biology and is highly interdisciplinary, using techniques and concepts from informatics, statistics, mathematics, chemistry, biochemistry, physics, and linguistics. It has many practical applications in different areas of biology and medicine.
It is well documented that the evolution of drug-resistant organisms are on the rise, and may lead to “superbugs,” untreatable by currently-available pharmaceuticals. This poses an extremely serious world-wide public health problem. Therefore, rapid and accurate determination of the resistance of a particular microorganism to the effects of different antibiotics is very important, with applications in a number of fields—from clinical microbiology and diagnostics of infectious diseases to the timely responses in case of a bioterrorism attack.
A number of classical microbiology techniques have been used to determine drug resistance. These techniques include monitoring organism proliferation in the presence of the drug, and the resulting biosynthesis of organism-specific molecules (DNA, proteins, etc.). For example, a change in optical density (turbidity) of culture suspensions is an indication of growth. These techniques typically take between 24 and 48 hours.
Recently, somewhat faster molecular level methods have been applied. Real-time quantitative PCR has been used to monitor the quantity of DNA in various gram-positive and gram-negative species in an effort to create an antibiotic susceptibility assay (J. Rolain, M. Mallet, P. Fournier, D. Raoult, and J. Antimicrob. Chemother. 54 (2004) 538-541, “Real-time PCR for universal antibiotic susceptibility testing.”). However, such PCR methods typically are by default “narrow-band,” i.e., they are generally used only after an organism has been identified in the sample.
In addition, techniques have been developed for labeling and characterizing biomolecules. Isotopes are atoms of the same element that have different masses. The isotopes of a particular element all have the same number of protons and electrons, but different number of neutrons. Isotopes provide a useful tool to scientists because although they have different masses, they do not differ significantly in their chemical behavior. Isotopic labeling is the technique used to label and track drugs or molecules that incorporate defined isotopes. Further, isotopic labeling has been employed with various drugs and biomolecules to study their structures, functions and in vivo processing or production. Isotopic labeling of drugs or biomolecules allows for an easy and effective way to study changes in biomolecules or drugs without impacting their functions.
Many of the existing systems and methods for determining drug resistance in microbes are neither rapid nor accurate. For instance, it is often necessary to wait a number of hours or days for microbes to go through various growth stages in order to characterize them. This is particularly problematic in both infectious disease and bioterrorism scenarios where time is of the essence in identifying, treating, or eradicating certain virulent and unknown pathogens. In addition, many existing tests and systems often produce false positives in identifying the existence or presence of various microbes. False identifications can lead to false diagnosis or further contaminations due to lack of containment or treatment.
For these reasons, what are needed are systems and methods for rapidly detecting, identifying, and characterizing drug-resistant and pathogenic microorganisms. Also needed are systems and methods that can accurately determine the presence or existence of such microbes. Further needed are systems and methods that are highly reliable and effective for providing accurate identifications and characterizations of drug-resistant and pathogenic microbes.